Let’s Git Started

Author

Affiliation

Prof. Matthew G. Son

University of South Florida

Installation

Git installation: Windows

1. For using Git/Github and Unix, install git bash for windows from:

https://git-scm.com/downloads

2. Configure git, your name and email address

git config --global user.name "Your Name"
git config --global user.email "you@example.com"

3. In Positron (VScode)

• Open command pallete with Ctrl + Shift + P
• Type “Terminal:Select Default Profile”
• Choose Git Bash for your default terminal

Git for macOS

1. Check if Xcode command line tools is not installed (if installed, skip)

• Open terminal

xcode-select --install

2. Configure git, your name and email address

git config --global user.name "Your Name"
git config --global user.email "you@example.com"

Note

Important

• You should also create an account on GitHub. Optionally, register with USF for a student previleges.

• Check if terminal understands git command. Type git on terminal and confirm no error message.

Github Login

Make sure you are able to login to Github.

Introduction to Git/GitHub

Why do we need Git?

Git

• Distributed version control system, created by Linus Torvalds (2005)

• “Track changes” made by team members, merge into main, etc.

• Considered a “must” for software development, and many data science projects.

• Has a learning curve, but it’s worth learning even for solo projects.

GitHub

• An online hosting platform that is based on Git system

• Easy to browse other repositories (public, free)

• Others: GitLab, Bitbucket, GitBucket, etc…

Why Git?

• Version control: track changes, revert to previous versions

• Collaboration: multiple people can work on the same project

• Backup: store your project on the cloud

• Portfolio: showcase your work to potential employers

• Open source: contribute to other projects

Is Git same as GitHub?

Nope.

• Git can be done completely locally (w/o internet).

• GitHub deploys Git to online cloud system.

Does Git/Github work with any files?

Git is primarily designed to handle text files and tracks changes line by line.

• It can upload binary files (e.g. images, pdfs), but doesn’t track differences like text files.

• GitHub has a file size limit (100MB)

• It is intended for code tracking; large data should be stored elsewhere

Git Terminology/workflow

Git shell commands

Git clone

Usually performed for the first time downloading from the remote repository.

git clone <repo_url>

# example
git clone https://github.com/example-user/example-repo.git

Git init

git init is used to initialize a new git repository from current working directory.

• This command creates a new hidden subdirectory named .git
• If you want to stop git, just remove this folder.

git init

Stage files

git add stages files for commit.

git add <filename> # stage specific files
git add -A # stage all files
git add -u # stage updated (modified, deleted) files only (not new)
git add . # stage new files only (not updated)

Make commit!

git commit creates your project’s version, or a hash block. You must provide message folling -m.

• As the name suggests, consider committing a serious process of your job, like signing a doc.

git commit -m "Commit message, describes the work / version"

Set remote repository

git remote add adds remote repository.

• origin is naming convention for Github remote repo.

git remote add <remote_name> <remote_url>

# example
git remote add origin https://github.com/username/repositoryname

Push to repository

git push sends your commit to the remote repository.

# When pushing for the first time
git push -u origin main 

# From then 
git push

Pull from repository

git pull does two operations altogether:

• fetch: download changes from the remote server
• merge: apply changes to your local file

git pull

# if job needes to be separated
git fetch
git merge

Git status / log

git status shows the status of changes as untracked, modified, or staged.

git status

git log shows the history of commits and its corresponding hashes.

git log

Git Reset

When you want to get back to previous commit (version) B

1. git reset B

• Changes made after B are unstaged
• Same as git reset --mixed B

2. git reset --soft B

• Changes after B are staged

3. git reset --hard B

• Match completely to commit B, all others discarded.

In Class Lab

1) My First Commit and Push to Github

1. Create your own folder for this class

• Name the folder nicely

• Create subfolders as:

  

• In R folder, create “my_first_R_code.R” file

2. Initialize Git on the folder

git init

and check the status and log on your directory:

git status
git log

3. Create your remote repository on Github website:

• Create public repo
• Name your repository nicely
• DO NOT ADD README FILE (leave it unchecked)
• Copy the address somewhere
  • It will look like https://github.com/yourGithubId/Reponame.git

4. Stage files (add files)

git add -A # stage all of files on the current directory

Check your status and see the difference

git status

5. Commit the staged version

It creates a “version”, a check-point of your project.

git commit -m "My first git commit"

Check your status and log also:

git status
git log

6. Name your local, initial branch as “main”

git branch -M main

Check your branches from current directory with

git branch

6. Set remote branch (your github) address as “origin”

git remote add origin https://github.com/yourGithubId/Reponame.git

Browse your branches now again, and check the differences

git branch
git branch -r
git branch -a

7. Push your local commit to upstream (remote repo)

git push -u origin main

Browse your github site, and see files are uploaded.

https://github.com/yourGithubId/Reponame.git

• Share the address to me.

Note

By default, git will only track files, not empty folders. Folders are tracked when files are in it.

2) My Second Commit and Push to Github

Now, make changes to your R\>my_first_R_code.R file:

• Write and modify the file: print("Hello world!") in the code and save.

• Then add, commit, and push to the github.

  • commit message: “My second commit”

• Browse history with:

git log

3) Reset changes (Time machine)

Now, suppose your second commit (version) was an error.

You can come back to previous commit by:

git reset <hash>

or

git reset head~1 # reset to 1 step before

At now, ONLY your local computer is back to the time when before the second commit. Your Github remote is in the future status (ahead) yet!

If you want your remote to be back to the first commit as well:

git push --force

Note that you should use --force option here.

4) Clone Class folder

1. Navigate to the Classroom subfolder

cd /path/to/classroom/subfolder
pwd # check your location

2. Clone the class folder to your machine

git clone <repository_url>

• I will be uploading class materials here from now on.

For future updates, use

# Make sure you are on the right folder
git pull

Github and IDE

When using github from other apps (e.g. Positron, VScode, etc), you’ll use PAT (personal access token) instead of password.

1. Install package from R and generate token

install.packages(usethis) # package installation
usethis::create_github_token()

2. Generate token from the page, with no expiration (or long enough)

• Copy the token to clipboard (you won’t see the token again)
  
• Store it somewhere temporarily
• Use it as your password from your Positron

More Git concepts

Three pull method

By default, git pull is

git fetch # download update but do not merge / apply changes to local
git merge # merge changes

git pull has three methods:

• git pull --merge

• git pull --rebase

• git pull --ff-only

git merge

Combines changes into a new merge commit. You will need to combine and resolve conflicts.

• B, C are your local change

Example: Git merge scenario

Content of file.txt

Alice edits the second line and commits and push to main first:

Bob also edits the same line, but did not pull Alice’s changes. He edits and commits locally:

When Bob tries to push changes with git push, Git will reject because his local branch is behind the remote.

Bob runs git pull which is git fetch and git merge: git shows the conflicts

The file.txt now contains conflict markers

To resolve conflict, Bob should modify the file manually.

Bob stages this file and commits the resolution:

After resolving, Bob pushes with git push.

git rebase

Git replays your local branch on top of the remote branch, creating a linear history:

Example: Git rebase scenario

Content of file.txt

Alice edits the second line and commits and push to main first:

Bob also edits the same line, but did not pull Alice’s changes. He edits and commits locally:

When Bob tries to push changes with git push, Git will reject because his local branch is behind the remote.

Bob runs git pull --rebase which is git fetch and git rebase:

Instead of creating a merge commit,

• git rewinds Bob’s local commit C

• applies Alice’s changes from remote (origin/main) B

• reapplies C on top of B

When there’s no conflict, (i.e., they did not change the same line of code) git pull –-rebase won’t raise any conflict message.

However, in our scenario, there’s conflict since both modified the same line, so:

• rebase is halted

• should be continued after conflict resolution

Similar to merge, conflict should be resolved manually.

The file.txt now contains conflict markers

To resolve conflict, Bob should modify the file manually.

Bob stages this file and continues the rebase (no commit)

git add file.txt
git rebase --continue

After that Bob pushes with git push. The history is linear.

git merge --ff-only

Used when you expect no conflicts.

When you want linear history and want to move your local branch pointer forward without modifying.

• Git rejects if there is any conflict

.gitignore

Git keep tracks all changes within the project directory

• New file, folder

• Modifications (changes or updates)

• Deletion

If there are files/folder you don’t want to track, specify them in .gitignore file.

git clean

If you want to remove untracked files:

git clean -nd # dry run (show what will be removed)
git clean -df # remove untracked files